Package: oncomix 1.34.0
Daniel Pique
oncomix: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.
Authors:
oncomix_1.34.0.tar.gz
oncomix_1.34.0.zip(r-4.7)oncomix_1.34.0.zip(r-4.6)oncomix_1.34.0.zip(r-4.5)
oncomix_1.34.0.tgz(r-4.6-any)oncomix_1.34.0.tgz(r-4.5-any)
oncomix_1.34.0.tar.gz(r-4.7-any)oncomix_1.34.0.tar.gz(r-4.6-any)
oncomix_1.34.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
oncomix/json (API)
NEWS
| # Install 'oncomix' in R: |
| install.packages('oncomix', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- exprNmlIsof - Human Breast Cancer RNA-sequencing data from TCGA - Adj. Normal Tissue
- exprTumIsof - Human Breast Cancer RNA-sequencing data from TCGA - Tumor Tissue
- queryRes - Oncogene Database Mapping Gene Symbol to UCSC ID
On BioConductor:oncomix-1.35.0(bioc 3.24)oncomix-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:26778874c5 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 172 | ||
| linux-devel-x86_64 | NOTE | 261 | ||
| source / vignettes | OK | 292 | ||
| linux-release-x86_64 | NOTE | 308 | ||
| macos-release-arm64 | NOTE | 208 | ||
| macos-oldrel-arm64 | NOTE | 154 | ||
| windows-devel | NOTE | 226 | ||
| windows-release | NOTE | 193 | ||
| windows-oldrel | NOTE | 209 | ||
| wasm-release | OK | 116 |
Exports:mixModelParamsoncoMixBimodaloncoMixIdealoncoMixTraditionalDEplotGeneHistscatterMixPlottoMatrixtopGeneQuants
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2ggrepelgluegtableIRangesisobandlabelinglatticelifecycleMatrixMatrixGenericsmatrixStatsmclustR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
